RetrogeneDB ID: retro_chof_2348

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_67490:3406..4012(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SLC35E3
• Ensembl ID: ENSCHOG00000013347
• Aliases: None
• Description: solute carrier family 35, member E3 [Source:HGNC Symbol;Acc:20864]

Sequence

>retro_chof_2348
ATCATAGCTATCCAGACTGTCTGCTACAAGGGAACCTTCTCCACCAGAGTAAAGCTCACACTGATTCCTATAACTTTAGG
TGTAATCCTAAGTCCTTACTACAATGTGAAGTTTAATTTCTTTGGAATGGTGTTTGCTGCTCTTGGTGTTTTAGTTACAT
CGCTTTATTGAGTGTGGTTAGGAACCAAACAGCTTGAACTGCAAGTAAACTCAATGCAGCTGCTGGACTACCAGGCACCG
ATGTCGCCGGCCATGCCGTTGGTCACTGTGCCCTTCTTTGAGCCCAAGTTCAGAGAAGGAGGAATATTTGGCCCCTGGTC
CATTTCTGCTTTGCTTATGTTGCTGCAATCTGGAATGACAGCTTTCATGGTGAATTTATCAATGTACTACATCATTGGGA
ACACTTTACCAGTTACCTACAACATGTTTCAACACTTGAAGTTCCATATCACATTATATGGAGGATATGGTTTATTGAAG
GACCCAATGTAAATTTAAATTAACCAGGGTCTTGGCATTTTCTGTACTTTGTTTGGCATTCTCACCTATACCCATTTTAA
ACTCAGTGAACAAGAAGGAAGTAAAAGTAAATTCATATAACATCCT

Alignment

ORF - retro_chof_2348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 58.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IVAIQTLCYKKTFSTGLQLR-IPITLGVILNSYYDVKFNFLGMVYAALGVLVTSLYQVWVGAKQHELQVN
          I.AIQT.CYK.TFST...L..IPITLGVIL..YY.VKFNF.GMV.AALGVLVTSLY.VW.G.KQ.ELQVN
Retrocopy IIAIQTVCYKGTFSTRVKLTLIPITLGVILSPYYNVKFNFFGMVFAALGVLVTSLY*VWLGTKQLELQVN

Parental  SMQLLYYQAPMSSAMLLVTVPFFEPVFGERGIFGPWSISALLMVLLSGVIAFMVNLSIYWIIGNTSPVTY
          SMQLL.YQAPMS.AM.LVTVPFFEP.F.E.GIFGPWSISALLM.L.SG..AFMVNLS.Y.IIGNT.PVTY
Retrocopy SMQLLDYQAPMSPAMPLVTVPFFEPKFREGGIFGPWSISALLMLLQSGMTAFMVNLSMYYIIGNTLPVTY

Parental  NMFGHLKFCITLFGGYVLLKDP--LSINQGLGILCTLFGILAYTHFKLSEQEGSKSKLVQRP
          NMF.HLKF.ITL.GGY.LLKDP....INQGLGI.CTLFGIL.YTHFKLSEQEGSKSK....P
Retrocopy NMFQHLKFHITLYGGYGLLKDPM*I*INQGLGIFCTLFGILTYTHFKLSEQEGSKSKFI*HP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_2348 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031919	1 retrocopy	retro_btau_642,
Choloepus hoffmanni	ENSCHOG00000013347	1 retrocopy	retro_chof_2348 ,
Cavia porcellus	ENSCPOG00000004322	3 retrocopies	retro_cpor_1404, retro_cpor_1487, retro_cpor_339,
Homo sapiens	ENSG00000175782	1 retrocopy	retro_hsap_513,
Gorilla gorilla	ENSGGOG00000012605	1 retrocopy	retro_ggor_473,
Mus musculus	ENSMUSG00000060181	1 retrocopy	retro_mmus_287,
Pan troglodytes	ENSPTRG00000005201	1 retrocopy	retro_ptro_383,
Pteropus vampyrus	ENSPVAG00000002545	1 retrocopy	retro_pvam_710,